SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.

By Manolo Gouy, Stéphane Guindon, Olivier Gascuel. 2010

5,738 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

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Citations in the corpus

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014, background): “Sequence-based protein alignment and homology detection has been extensively studied and widely applied to many biological problems such as homology modeling [1-4], phylogeny inference [5-7] and protein function prediction [8-10].”
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega (2011, background): “Further, there are several very high-quality alignment viewers and editors such as Jalview (Clamp et al, 2004) and Seaview (Gouy et al, 2010) that read Clustal Omega output or which can call Clustal Omega directly.”
Molecular Evolution of Zika Virus during Its Emergence in the 20th Century (2014, neutral): “3 [30].”
New supraordinal classification of Foraminifera: Molecules meet morphology (2013, neutral): “(Gouy et al., 2010).”
Comparative genomics reveals insights into avian genome evolution and adaptation (2014, neutral): “2) (158) then back translated to nucleotides.”
The floating Sargassum (Phaeophyceae) of the South Atlantic Ocean – likely scenarios (2017, positive): “2 (Gouy et al. 2010).”
Roholtiella , gen. nov. (Nostocales, Cyanobacteria)—a tapering and branching cyanobacteria of the family Nostocaceae (2015, methodology): “…3.2.2 (ronquist et al. 2012), maximum likelihood analysis in PhyMl 3.0 (Guindon et al. 2010), and maximum parsimony analysis in Seaview 4.5.1 (Gouy et al. 2010). for the Bayesian analysis, two runs of eight Markov chains were executed for 5 million generations with default parameters,…”
Evolution of nutritional modes of Ceratobasidiaceae (Cantharellales, Basidiomycota) as revealed from publicly available ITS sequences (2013, methodology): “All sequences were aligned with MAFFT (Katoh & Toh 2008) and inspected by use of the program Seaview (Gouy et al. 2010) to identify short and lowquality ITS sequences.”
A new ensemble coevolution system for detecting HIV-1 protein coevolution (2015, neutral): “3 [56].”
Clustal Omega (2014, methodology): “FASTA format is very convenient and compact, and widely used by other packages that can be used to display or analyze an alignment, such as SeaView (Gouy et al., 2010) or JalView (Troshin et al., 2011).”
Pitfalls in supermatrix phylogenomics (2017, positive): “This strategy is implemented in transAlign (Bininda-Emonds 2005), TranslatorX (Abascal et al. 2010), and Seaview 4 (Gouy et al. 2010), for example.”
The genetic diversity, phylogeography and morphology of Elphidiidae (Foraminifera) in the Northeast Atlantic (2016, methodology): “A Bio Neighbor-Joining (BioNJ) tree (Gascuel, 1997) was constructed using Seaview 4 (Gouy et al., 2010) with 1000 bootstrap (BS) replicates (Felsenstein, 1985).”